pyCADD.Demand package

Submodules

pyCADD.Demand.cli module

pyCADD.Demand.config module

class pyCADD.Demand.config.BaseQueryCfg(pdb_list)[source]

Bases: object

__init__(pdb_list)[source]

get_query()[source]

class pyCADD.Demand.config.BaseQueryPDB(uniprot_id: str)[source]

Bases: object

__init__(uniprot_id: str) → None[source]

get_query()[source]

class pyCADD.Demand.config.QueryConfigKeys[source]

Bases: object

DATA_KEYS = ['data', 'entries']

PDBID_KEYS = ['rcsb_id']

TITLE_KEYS = ['struct', 'title']

RESOLUTION_KEYS = ['rcsb_entry_info', 'resolution_combined', 0]

AUTHOR_KEYS = ['rcsb_primary_citation', 'rcsb_authors']

REFERENCE_KEYS = ['rcsb_primary_citation', 'title']

REF_DOI_KEYS = ['rcsb_primary_citation', 'pdbx_database_id_DOI']

POLYMER_ENTITY_NUM_KEYS = ['rcsb_entry_info', 'deposited_polymer_entity_instance_count']

NONPOLYMER_ENTITY_NUM_KEYS = ['rcsb_entry_info', 'deposited_nonpolymer_entity_instance_count']

POLYMER_ENTITY_KEYS = ['polymer_entities']

POLYMER_NAME_KEYS = ['rcsb_polymer_entity', 'pdbx_description']

POLYMER_TYPE_KEYS = ['entity_poly', 'rcsb_entity_polymer_type']

POLYMER_MUTATION_NUM_KEYS = ['entity_poly', 'rcsb_mutation_count']

POLYMER_MUTATION_KEYS = ['rcsb_polymer_entity', 'pdbx_mutation']

POLYMER_CHAIN_ID_KEYS = ['entity_poly', 'pdbx_strand_id']

POLYMER_UNIPROT_ID_KEYS = ['rcsb_polymer_entity_container_identifiers', 'uniprot_ids']

NONPOLYMER_ENTITY_KEYS = ['nonpolymer_entities']

NONPOLYMER_NAME_KEYS = ['nonpolymer_comp', 'chem_comp', 'name']

NONPOLYMER_ID_KEYS = ['nonpolymer_comp', 'chem_comp', 'id']

NONPOLYMER_SMILES_KEYS = ['nonpolymer_comp', 'rcsb_chem_comp_descriptor', 'SMILES']

NONPOLYMER_CHAIN_ID_KEYS = ['rcsb_nonpolymer_entity_container_identifiers', 'auth_asym_ids']

__init__() → None

pyCADD.Demand.core module

pyCADD.Demand.core.parse_uniport(uniprot_file_path: str)[source]

pyCADD.Demand.core.query_uniprot_id_on_pdb(uniprot_id: str, save_dir: str = None) → list[source]

pyCADD.Demand.core.query_pdb(pdb_list: list, save_path: str = None, query_cfg: BaseQueryCfg = None)[source]

pyCADD.Demand.core.get_nested_value(data, keys)[source]

class pyCADD.Demand.core.QueryClient(uniprot_id: str = None, pdb_list_file: str = None, save_dir: str = None)[source]

Bases: object

__init__(uniprot_id: str = None, pdb_list_file: str = None, save_dir: str = None) → None[source]

property uniprot_save_dir

property pdb_save_dir

get_apo()[source]

get_mutations()[source]

query()[source]

clean_pdb_data(del_mutations: bool = True, del_ignore_lig: bool = True, cutoff: float = None)[source]

清洗 pdb 数据:

去除Apo晶体
去除配体未结合于目标链的晶体
去除非WideType晶体(optional)
去除非配体的小分子(e.g. DMS, optional)
去除分辨率高于Cutoff的晶体(optional)

get_mutation_pdb()[source]

generate_inputfile(path: str, _format: str = None)[source]

Module contents